added pipeline commands which involved change to command factory and command class...

[mothur.git] / unweighted.cpp

diff --git a/unweighted.cpp b/unweighted.cpp
index 2afc4a71486617b61308b651fef413895ba05b54..da6ad2c1cc0bd6cea255546890b303888a46d6d7 100644 (file)
--- a/unweighted.cpp
+++ b/unweighted.cpp
@@ -170,10 +170,12 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                EstOutput results; results.resize(num);
                
                int count = 0;
+               int numLeaves = t->getNumLeaves();
                int total = num;
                int twentyPercent = (total * 0.20);
                if (twentyPercent == 0) { twentyPercent = 1; }
                
+               
                for (int h = start; h < (start+num); h++) {
                
                        if (m->control_pressed) { return results; }
@@ -181,6 +183,9 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                        double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
                        double totalBL = 0.00;  //all branch lengths
                        double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
+                       map<int, double> tempTotals; //maps node to total Branch Length
+                       map<int, int> nodePcountSize; //maps node to pcountSize
+                       map<int, int>::iterator itCount;
                                
                        for(int i=0;i<t->getNumNodes();i++){
                        
@@ -195,15 +200,38 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                        map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
                                        if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } 
                                }
+
+                               nodePcountSize[i] = pcountSize;
                                
-                               if (pcountSize == 0) { }
-                               else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength());   }
+                               if (pcountSize == 0) { ; }
+                               else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength()); }
+                                                               
+                               //if you are a leaf from a users group add to total
+                               if (i < numLeaves) {
+                                       if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) {  
+                                               totalBL += abs(t->tree[i].getBranchLength()); 
+                                       }
+                                       tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
+                               }else{ //if you are not a leaf 
+                                       //do both your chidren have have descendants from the users groups? 
+                                       int lc = t->tree[i].getLChild();
+                                       int rc = t->tree[i].getRChild();
                                        
-                               if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {  
-                                       totalBL += abs(t->tree[i].getBranchLength()); 
+                                       //if yes, add to total your childrens branchLengths and your childrens tempTotals
+                                       if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+                                               totalBL += tempTotals[lc] + tempTotals[rc]; 
+                                               if (t->tree[i].getBranchLength() != -1) {
+                                                       tempTotals[i] = abs(t->tree[i].getBranchLength());
+                                               }else {
+                                                       tempTotals[i] = 0.0;
+                                               }
+                                               //tempTotals[i] = tempTotals[lc] + tempTotals[rc]; 
+                                       }else { //if no, your tempTotal is your childrens temp totals
+                                               tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength()); 
+                                       }
                                }
                        }
-       
+                       
                        UW = (UniqueBL / totalBL);  
        
                        if (isnan(UW) || isinf(UW)) { UW = 0; }
@@ -384,6 +412,7 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                int count = 0;
                int total = num;
                int twentyPercent = (total * 0.20);
+               int numLeaves = t->getNumLeaves();
                
                Tree* copyTree = new Tree;
                
@@ -400,6 +429,8 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                        double UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
                        double totalBL = 0.00;  //all branch lengths
                        double UW = 0.00;               //Unweighted Value = UniqueBL / totalBL;
+                       map<int, double> tempTotals; //maps node to total Branch Length
+                       map<int, int> nodePcountSize; //maps node to pcountSize
                                
                        for(int i=0;i<copyTree->getNumNodes();i++){
                        
@@ -415,12 +446,36 @@ EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombo
                                        if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } } 
                                }
                                
+                               nodePcountSize[i] = pcountSize;
+                               
                                if (pcountSize == 0) { }
                                else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());     }
+                               
+                               //if you are a leaf from a users group add to total
+                               if (i < numLeaves) {
+                                       if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) {  
+                                               totalBL += abs(copyTree->tree[i].getBranchLength()); 
+                                       }
+                                       tempTotals[i] = 0.0;  //we don't care about you, or we have already added you
+                               }else{ //if you are not a leaf 
+                                       //do both your chidren have have descendants from the users groups? 
+                                       int lc = copyTree->tree[i].getLChild();
+                                       int rc = copyTree->tree[i].getRChild();
                                        
-                               if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0)) {  
-                                       totalBL += abs(copyTree->tree[i].getBranchLength()); 
+                                       //if yes, add to total your childrens branchLengths and your childrens tempTotals
+                                       if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
+                                               totalBL += tempTotals[lc] + tempTotals[rc]; 
+                                               if (copyTree->tree[i].getBranchLength() != -1) {
+                                                       tempTotals[i] = abs(copyTree->tree[i].getBranchLength());
+                                               }else {
+                                                       tempTotals[i] = 0.0;
+                                               }
+                                               //tempTotals[i] = tempTotals[lc] + tempTotals[rc]; 
+                                       }else { //if no, your tempTotal is your childrens temp totals
+                                               tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength()); 
+                                       }
                                }
+
                        }
                
                        UW = (UniqueBL / totalBL);